Scully meets Special Agent John Doggett, the leader of an FBI task force organized to conduct a search for Mulder. Although the search ultimately proves unsuccessful, Doggett is assigned to the X-files and works with Scully to look for explanations to several cases. When Scully learns that several women have reportedly been abducted and impregnated with alien babies, she begins to question her own pregnancy and fears for her unborn child.
Doggett introduces Scully to Monica Reyes, an FBI specialist in ritualistic crime, shortly before Mulder's deceased body suddenly appears in a forest at night. Following Mulder's funeral, Assistant Director Skinner is threatened by Alex Krycek that he must kill Scully's baby before it is born. Billy Miles, a multiple abductee who disappeared on the same night as Mulder, is returned deceased but his dead body is apparently resurrected and restored to full health. Mulder also returns from death, with Scully supervising his recovery. Fully rejuvenated, Mulder investigates several X-files, against orders to do so, but soon quits the FBI and leaves Doggett in charge of the cases. Mulder continues to provide input on an unofficial capacity. With Scully on maternity leave, Doggett is assigned a new partner, an inexperienced agent who is obsessed with the X-files, but the relationship is only temporary.
Reluctantly accepting Krycek's assistance, Mulder, Doggett and Skinner learn that an alien virus recently created in secret by members of the American government has replaced several humans, including Billy Miles and several high-ranking FBI personnel, with alien supersoldiers. Krycek claims that the soldiers are virtually unstoppable aliens who want to make sure that humans will not survive the colonisation of Earth. They have somehow learned that Scully's baby is a miraculously special child and are afraid that it may be greater than them. They have only recently learned of the baby's importance, which is why Krycek told Skinner to kill the unborn child earlier. When Billy Miles arrives at the FBI Headquarters, Mulder, Doggett, Skinner and Krycek help Scully to escape with Special Agent Reyes who drives her to a remote farm. Shortly after Skinner kills Krycek, Scully delivers an apparently normal baby while the alien supersoldiers surround her. Without explanation, the aliens leave the area as Mulder arrives. While Doggett and Reyes report to the FBI Headquarters, Mulder takes Scully and her newborn baby back to her apartment.
|No.||Episode Name / Summary|
An FBI task force is organized to hunt for Mulder but Scully suspects the task force leader, Special Agent John Doggett, and instead chooses to search for her lost partner with Skinner.
As the FBI task force continues to look for Mulder, they encounter an alien bounty hunter among them. Scully helps to defeat the alien and, after the task force is called off, she is surprised to learn that John Doggett, the leader of the team, has been assigned to the X-Files.
Investigating his first X-File case, Doggett travels with Scully to Idaho where a married couple were brutally murdered by a human-sized bat.
In a small remote town in Utah, Scully is trapped by the town's residents, a religious cult that worships a parasitic creature inserted near its host's spine.
After a boy who disappeared ten years ago suddenly returns without explanation, the case echoes back to certain incidents in Doggett's past but he and Scully discover that the boy hasn't aged a day.
An old friend of John Doggett and formerly successful lawyer finds himself in jail for the murder of his wife, an incident he has no memory of. As he starts to live days in reverse, he realizes that he has been granted a second chance.
While Scully takes time off to deal with the early stages of her pregnancy, Doggett and Skinner attempt to avert the mysterious murder spree of a religious cult leader who kills his victims in their sleep.
Looking for plausible scientific explanations, Scully and Doggett investigate an assassin with seemingly impossible visual abilities but they soon learn that there's more to the case than meets the eye.
Scully and Doggett encounter an apparently indestructible killer, whose body is transforming into a machine.
As Scully tries to keep an open mind, she and Doggett piece together evidence of a murdering Indian mystic who hides in the stomachs of his victims.
Hoping to determine Mulder's whereabouts, Doggett investigates a case that Mulder kept secret from Scully involving a soul eater, a creature that can consume the sicknesses of others.
In a race against time, Doggett leads a team of professionals into the Boston subway system in search of a murderer. However, Scully discovers that a killer sea organism is responsible and Doggett is infected.
Scully becomes personally involved when she encounters several women who had no way of naturally conceiving but who claim to have been abducted and impregnated with alien babies.
|8ABX14||"This Is Not Happening"
With assistance from a specialist in ritualistic crime, Scully, Doggett and Skinner discover a group of UFO enthusiasts who help returned abductees recover.
Shortly after Mulder is buried, a former abductee's deceased body returns and is miraculously resurrected, offering hope for Mulder's recovery. Meanwhile, Krycek threatens Skinner that he must kill Scully's unborn child.
Although Mulder is denied reassignment to the X-Files, he nevertheless investigates a man who was shot before he could inform the President that alien invasion has begun.
While Scully recovers from complications related to her pregnancy, Reyes contacts Mulder about a man seemingly connected to the unsolved murder of Doggett's son
Despite orders to stay away from the X-Files, Mulder finds himself stranded on a quarantined oil rig with Doggett where the crew have been infected by an alien virus that he has encountered many times before.
With Scully on maternity leave, Doggett is assigned an inexperienced new partner who is obsessed with the X-files. Together, they are trapped in an underground tunnel by a creature that can assume a human appearance and uses snake venom to blind its victims.
Mulder, Doggett and Skinner investigate lingering questions concerning Scully's pregnancy, reluctantly accepting help from Krycek as an alien who was once human pursues Scully and her unborn child.
Mulder, Doggett and Skinner discover that high-ranking FBI personnel have been transformed into alien "super-soldiers" while Reyes fears for Scully's unborn child as she prepares to deliver the baby on a remote farm.
- David Duchovny as Special Agent Fox Mulder (12/21 episodes)
- Gillian Anderson as Special Agent Dana Scully (20/21 episodes)
- Robert Patrick as Special Agent John Doggett (21/21 episodes)
- Mitch Pileggi as Assistant Director Walter Skinner (12/21 episodes)
- Annabeth Gish as Special Agent Monica Reyes (4/21 episodes)
- Nicholas Lea as Alex Krycek (3/21 episodes)
- James Pickens, Jr. as Deputy Director Alvin Kersh (7/21 episodes)
- Tom Braidwood as Melvin Frohike (6/21 episodes)
- Bruce Harwood as John Fitzgerald Byers (6/21 episodes)
- Dean Haglund as Richard Langly (6/21 episodes)
- Kirk B.R. Woller as Agent Gene Crane (5/21 episodes)
- Zachary Ansley as Billy Miles (3/21 episodes)
- Adam Baldwin as Knowle Rohrer (3/21 episodes)
- Jeff Gulka as Gibson Praise (2/21 episodes)
- Sheila Larken as Margaret Scully (2/21 episodes)
- This season also takes place simultaneously as Season 1 of The Lone Gunmen.
- This was David Duchovny's last season as a regular in the original run.
- This is the only season that William B. Davis (Cigarette Smoking Man) did not appear in.